LintR

Lint Workflow

This GitHub Actions workflow performs linting tasks for an R package. It runs on a docker container instance using admiralci images (ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest) for the R environment.

Workflow Triggers

This workflow is triggered in the following ways:

Manual Dispatch: You can manually trigger the workflow using the “workflow_dispatch” event.
Workflow Call: The workflow can also be triggered by another workflow using the “workflow_call” event.

Workflow Inputs

The workflow accepts the following inputs during manual dispatch or workflow call:

r-version: The version of R to use, with options ‘4.1’, ‘4.2’, and ‘4.3’.
lint-all-files: Boolean indicating whether to lint all files every time.
latest-lintr: Boolean indicating whether to install the latest lintr CRAN release.
install-package: Boolean indicating whether to install the R package locally.

Workflow Setup

Concurrency: Lint jobs are organized by the pull request number or branch.
Cancel-in-progress: Allows canceling in-progress lint jobs.

Job: `lint`

This job performs linting tasks.

Steps

Get branch names: Gets the branch names using the tj-actions/branch-names action.
Checkout repo (PR): Checks out the repository for pull requests.
Checkout repository: Checks out the repository for non-pull request events.
Normalize inputs: Normalizes the R version input.
Restore cache: Restores the cache for staged dependencies.
Run Staged dependencies: Runs staged dependencies action to set up the environment.
Install dependencies from DESCRIPTION: install dependencies from DESCRIPTION (in case of missing dependencies in parent admiralci docker image)
Install latest release of lintr: Installs the latest release of lintr from the CRAN repository if specified.
Install package: Installs the R package locally if specified.
Changed files: Gets the list of changed files using the Ana06/get-changed-files action.
Lint: Performs linting using lintr on the R package. Excludes files based on the changed files list.
Error if lints are detected: Raises an error if lints are detected, prompting a review and adjustment of the code.

Note : a .lintr file can be configured at the upstream repository level, to be able for example to exclude some lint rules such as this example :

exclusions: list(
    "R/data.R" = Inf,
    "inst" = list(undesirable_function_linter = Inf),
    "vignettes" = list(undesirable_function_linter = Inf)
  )

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